BIOEE1780 Population Genetics 1 and 2

The genetic variation within and among populations and the changes in frequencies through evolution.

The position of a gene on a chromosome.

One copy of a gene at a locus.

Pair of alleles at a single locus, determining the genotype.

• The hypothesis that there is no statistically significant relationship between the set of given observations. It is presumed to be true until an alternative hypothesis is proven more likely.
• The null hypothesis for the Hardy-Weinberg equilibrium (population genetics) is that no evolution is happening and that there are no changes.

Changes in population’s allele or genotype frequencies over time.

• P + q = 1 (p being the frequency of the dominant allele by convention and q the frequency of the recessive allele)
• Thus p2 + 2pq + q2 = 1
• For three alleles, p + q + r = 1 and the same goes for its squared version.
• By comparing natural populations with the hardy weinberg equilibrium, we can detect evolution.
• NOTE: Check how to do the math for this from observations.

• No mutation
• No selection
• No migration (gene flow)
• Infinite population size (this negates random drift)
• Random mating
• Forces (evolutionary) that change the genetic frequency are violations of these assumptions.

• Natural selection
• Non-random mating
• Genetic drift
• Gene flow
• Mutation

• Calculate p and q by dividing allele frequency by total alleles (individuals x 2 if diploid)
• Calculate expected frequencies of p2 + 2pq + q2
• Calculate expected number of genotypes by multiplying the values by total number of individuals.
• Do Chi square test: sum (observed-expected)2/expected
• Chi square threshold is 3.84
• If your chi square is larger, you have statistical significance. This means that microevolutionary forces are pushing the population out of equilibrium.

Refers to the number of copies of unique chromosomes in a cell (n). Normal human somatic cells are diploid (2n), they have two copies of 23 chromosomes.

A segment of DNA whose nucleotide sequences code for proteins, RNA or regulate the expression of other genes.

Is the process that takes place when RNA polymerase reads a coding sequence of DNA and produces a complementary strand of RNA, called messenger RNA. mRNA carries genetic information from DNA to the ribosome,

It is an essential macromolecule for all known forms of life. It differs from DNA by having ribose instead of deoxyribose and uracil instead of thymine.

A single base changes from one nucleotide to another. (substitution)

A segment of DNA is inserted into the middle of an existing sequence.

A segment of DNA is deleted.

A segment of DNA is copied a second time. Entire genes, or even genomes can be duplicated.

A segment of DNA is flipped around and inserted backwards into its original position.

Two chromosomes are joined together as one.

Chromosomes are duplicated or lost, leading to an abnormal number of chromosomes.

Stretches of DNA located near a gene, either immediately upstream(promoter region), or downstream, or inside an intron, that influence the expression of the gene. They often code for the binding sites for one or more transposable factors.

Sequences of DNA that are far away from the focal gene. These elements generally code for a protein, microRNA, or other diffusible molecule that affects the expression of that gene.

Alters the production of the gene, and thus its function or activity.

• They affect the binding affinity of promoters, activators, repressors etc.
• Which affects the timing, location, or level of expression of that gene.
• Alters the developmental or environmental context where the gene is expressed.

Alters the binding affinity and thus the activity of a promoter, activator, repressor etc.

Alters where when and to what extent inhibitory, activating or other trans acting regulatory factors are expressed.

• Alters where when and to what extent an endocrine signal is produced,
• Which affects the timing, location, or level of expression of that gene.
• Alters the developmental or environmental context where the gene is expressed.

• Somatic mutations are not passed down (except for vegetative reproduction in plants)
• Germ-line mutations are passed down.

A deleterious mutation affecting gene activity or expression in one chromosome may be masked by the presence of a functional copy on the other chromosome. This isn’t the case for haploid organisms like bacteria.

When they occur in non-coding regions (cis or trans regulatory regions)

• Genetic recombination and independent assortment of chromosomes generates extraordinary variation in the gametes of sexually reproducing organisms.
• In addition, the merging of egg and cell (random) results in even greater genetic diversity in siblings.

The simultaneous occurrence of two or more discrete phenotypes within a population. This can, in its simplest form, be a result of different allele combinations of a single gene leading to different phenotypes. In more complex forms, it could result from the interactions between a multitude of genes and the environment.

• A trait for which multiple distinct phenotypes can arise from a single genotype based on environmental circumstances.
• These often result from developmental threshold mechanisms.
• Remember from poly-phenotype

• Polygenic traits that result in a continuous distribution of measurable phenotypes.
• (Such as height)

• This is a central assumption in population genetics. While sexual selection does occur, this generally does not affect the concept of random mating.
• This is because random mating is limited to the scope of a specific locus. Random mating only implies that the probability of one sperm containing one allele reaching the egg is equal to the probability of another sperm containing another allele reaching the egg.

Study of continuous phenotypic traits and their underlying evolutionary mechanisms.

• Hardy Weinberg equilibrium results in higher frequency of heterozygotes. When you combine environmental variation of a phenotype with the different phenotypes in the population, you get a continuous normal distribution.
• This is why Vp = Vg + Ve

• They’re polygenic.
• They depend on non-additive interactions between alleles at the loci that affect the phenotypic trait. (epistasis)
• They are shaped by the interaction between the alleles and the environment (phenotypic plasticity)

• Additive genetic variance.
• Simple genetic variation. Multiple genes that exert influence in a linear fashion
• Narrow sense heritability Va/Vp

• Variance is a statistical measure of the dispersion of trait values about their mean. Traits exhibit high variation have high variance.
• In genetics, variance is calculated from the formula:
• Vp (variance in the phenotypic trait) = Vg (genetic variance) + Ve (difference arising from environmental conditions)
• For different traits the relative values of Vg and Ve differ.

• (H squared)
• Used to determine the heritability of a trait
• The proportion of the total phenotypic variance that is attributable to genetic variance, where genetic variance is represented in its entirety as a single value. Vg/Vp or Vg/(Vg+Ve)

Because it represents all genetic variance as a single value, it assumes that the entire genome of a parent is transmitted to an offspring. This is obviously wrong for sexually reproducing organisms. Only some of the genetic variation actually contributes to parent - offspring resemblance, and only this portion contributes to evolution.

• (h squared)
• Is the proportion of the total phenotypic variance of a trait attributable to the additive effects of alleles. This is the component that causes offspring to resemble their parents and contributes to evolution.
• Vg = Va (additive genetic variance) + Vd (variance due to dominance effect + Vi (epistatic interactions)

The effect of a mutation is dependent on mutations on other genes.

Additive genetic influence (A) describes the effect of multiple genes that exert influence in a linear or additive fashion. Non-additive genetic factors (NA), by contrast, describe interactive effects of different alleles and include genetic dominance (within locus interaction) and epistasis (across locus interaction).

• Mean of offspring vs. mean of parents. Higher the slope, higher the heritability.
• Selection results in a shift in the x axis in the positive direction. The larger the slope is, the higher the increase in the trait in the offspring. Since the component of variation that causes a population to evolve in response to evolution is by definition narrow sense heritability, the slope will represent narrow sense heritability.

Narrow sense heritability.

Adaptation rate depends on whether the allele is dominant, recessive, additive, or co-dominant.

• First individual will be heterozygous.
• Homozygous dominant will only arise when there is enough heterozygotes in the population.
• Evolution will slow down when most of the population is heterozygous and homozygous dominant. However, there will be no selective pressure pushing A1 into fixation.
• Homozygous recessive will still occur, but will be eliminated by selection.
• This is an example for why selection is not always effective in removing deleterious alleles.
• S curve but NEVER FIXES due to sheltering of recessive alleles.

All are S curves.

• First individual will be heterozygous.
• Recessive allele will not be expressed (homozygote will not arise) until enough heterozygotes in the population. However, this will take much longer than the dominant case, as no selective pressure will be operating. It’s also likely that the advantageous allele will be lost to drift before anything occurs.
• If a homozygous recessive does occur by pure chance (drift!) it will have remarkably high fitness. It will then very rapidly increase until it becomes fixed.

• If Va is small. Or if Ve is very large.
• Explain rate of adaptation when A1 is overdominant and advantageous

• Heterozygotes have some advantage over homozygous recessive, but not a low, so evolution proceeds kind of slowly. (slower than dominant and advantageous but faster than recessive, S curve)
• When the frequency of heterozygotes is high enough, homozygous dominants will occur.
• As homozygous dominants have the highest fitness, the codominant A1 with highest fitness will eventually become fixed.

• Initial rate is the same as dominant, but slows down earlier at 0.5.
• No fixation.

• AA hosts are more likely to die from malaria.
• AS have slightly lower oxygen carrying capacity, but are less likely to die from malaria.
• SS individuals suffer from sickle cell anemia and are very sick.
• In areas where malaria is endemic, WAS > WAA > WSS
• Malaria and sickle cell anemia overlap. This shows that fitness is context dependent.

white plus red is pink

heterozygote is most advantageous

• slow increase
• fixation

• rapid increase
• no fixation

• medium increase
• fixation

• rapid increase, 
• stops at 0.5 
• genetic variation maintained

• rapid decrease 
• but never lost

• rapid decrease 
• fully lost

• medium decrease
• eventually fully lost